Well, I hope you don't have any spirits living in your home with you.
Let's pray for good angels at the very least.
Gracie does a sound in her throat that is kind of like a growl but slower when she is trying to "talk" to me and tell me something. I have to then try to decide what she is saying. Her growl is more like a purr, much faster and more excited than her "talking" voice.
It does sound like your puppy is seeing something that is upsetting. Eventually he will either show you what it is or decide to ignore it.